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BrassicaEDB: A Gene Expression Database for Brassica Crops

文献类型： 外文期刊

作者： Chao, Haoyu 1 ; Li, Tian 3 ; Luo, Chaoyu 1 ; Huang, Hualei 5 ; Ruan, Yingfei 3 ; Li, Xiaodong 1 ; Niu, Yue 1 ; Fan, Yongh 1 ;

作者机构： 1.Southwest Univ, Coll Agron & Biotechnol, Chongqing 400715, Peoples R China

2.Southwest Univ, Inst Innovat & Entrepreneurship, Chongqing 400715, Peoples R China

3.Southwest Univ, State Key Lab Silkworm Genome Biol, Chongqing 400715, Peoples R China

4.Southwest Univ, Chongqing Key Lab Microsporidia Infect & Control, Chongqing 400715, Peoples R China

5.Chongqing Acad Agr Sci, Inst Characterist Crop Res, Chongqing 402160, Peoples R China

6.Southwest Univ, Acad Agr Sci, Chongqing 400715, Peoples R China

关键词： BrassicaEDB; Brassica napus; gene expression profile; RNA-Seq

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：4.9； 五年影响因子：5.6 ）

ISSN：

年卷期： 2020 年 21 卷 16 期

页码：

收录情况： SCI

摘要： The genusBrassicacontains several economically important crops, including rapeseed (Brassica napus, 2n= 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed theBrassicaExpression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including "eFP", "Treatment", "Coexpression", and "SRA Project" modules based on gene expression profiles and "Gene Feature", "qPCR Primer", and "BLAST" modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

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